* using log directory ‘/Users/ripley/R/packages/tests-devel/OhdsiReportGenerator.Rcheck’
* using R Under development (unstable) (2025-12-16 r89178)
* using platform: aarch64-apple-darwin25.2.0
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.6.3.2)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.2
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘OhdsiReportGenerator/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OhdsiReportGenerator’ version ‘1.1.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OhdsiReportGenerator’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [60s/89s]
 [61s/89s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("OhdsiReportGenerator")
  Loading required package: OhdsiReportGenerator
  Connecting using SQLite driver
  
  
  processing file: assure_presentation.qmd
  output file: assure_presentation.knit.md
  
  Closing database connection
  pandoc 
    to: revealjs
    output-file: assure_presentation.html
    standalone: true
    self-contained: true
    wrap: none
    default-image-extension: png
    html-math-method:
      method: mathjax
      url: >-
        https://cdn.jsdelivr.net/npm/mathjax@2.7.9/MathJax.js?config=TeX-AMS_HTML-full
    slide-level: 2
    variables: {}
    
  metadata
    link-citations: true
    width: 1050
    height: 700
    margin: 0.1
    center: false
    navigationMode: linear
    controlsLayout: edges
    controlsTutorial: false
    hash: true
    history: true
    hashOneBasedIndex: false
    fragmentInURL: false
    transition: none
    backgroundTransition: none
    pdfSeparateFragments: false
    lang: en
    auto-stretch: true
    title: ASSURE Analysis
    scrollable: true
    theme:
      - default
      - presentation_style.scss
    logo: img/logo.png
    title-slide-attributes:
      data-background-color: '#EB1700'
    footer: ASSURE Analysis
    slideNumber: true
    showSlideNumber: all
    menu:
      side: left
      numbers: true
    
  [WARNING] Could not fetch resource img/logo.png
  ERROR: Refusing to remove directory /private/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/RtmpUGvSgG/working_dir/RtmpCTXGIR/presentation/assure_presentation_files that isn't a subdirectory of /var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/RtmpUGvSgG/working_dir/RtmpCTXGIR/presentation
  
  Stack trace:
      at safeRemoveDirSync (file:///Applications/quarto/bin/quarto.js:2540:11)
      at file:///Applications/quarto/bin/quarto.js:114469:9
      at Array.forEach (<anonymous>)
      at renderCleanup (file:///Applications/quarto/bin/quarto.js:114467:23)
      at file:///Applications/quarto/bin/quarto.js:115409:44
      at withTiming (file:///Applications/quarto/bin/quarto.js:18977:21)
      at Object.complete (file:///Applications/quarto/bin/quarto.js:115409:9)
      at eventLoopTick (ext:core/01_core.js:178:7)
      at async Object.onPostProcess (file:///Applications/quarto/bin/quarto.js:123992:28)
      at async renderFileInternal (file:///Applications/quarto/bin/quarto.js:123976:3)
  Saving _problems/test-Backwards-47.R
  
  
  processing file: assure_presentation.qmd
  output file: assure_presentation.knit.md
  
  Closing database connection
  pandoc 
    to: revealjs
    output-file: assure_presentation.html
    standalone: true
    self-contained: true
    wrap: none
    default-image-extension: png
    html-math-method:
      method: mathjax
      url: >-
        https://cdn.jsdelivr.net/npm/mathjax@2.7.9/MathJax.js?config=TeX-AMS_HTML-full
    slide-level: 2
    variables: {}
    
  metadata
    link-citations: true
    width: 1050
    height: 700
    margin: 0.1
    center: false
    navigationMode: linear
    controlsLayout: edges
    controlsTutorial: false
    hash: true
    history: true
    hashOneBasedIndex: false
    fragmentInURL: false
    transition: none
    backgroundTransition: none
    pdfSeparateFragments: false
    lang: en
    auto-stretch: true
    title: ASSURE Analysis
    scrollable: true
    theme:
      - default
      - presentation_style.scss
    logo: img/logo.png
    title-slide-attributes:
      data-background-color: '#EB1700'
    footer: ASSURE Analysis
    slideNumber: true
    showSlideNumber: all
    menu:
      side: left
      numbers: true
    
  [WARNING] Could not fetch resource img/logo.png
  ERROR: Refusing to remove directory /private/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/RtmpUGvSgG/working_dir/RtmpCTXGIR/presentation/assure_presentation_files that isn't a subdirectory of /var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/RtmpUGvSgG/working_dir/RtmpCTXGIR/presentation
  
  Stack trace:
      at safeRemoveDirSync (file:///Applications/quarto/bin/quarto.js:2540:11)
      at file:///Applications/quarto/bin/quarto.js:114469:9
      at Array.forEach (<anonymous>)
      at renderCleanup (file:///Applications/quarto/bin/quarto.js:114467:23)
      at file:///Applications/quarto/bin/quarto.js:115409:44
      at withTiming (file:///Applications/quarto/bin/quarto.js:18977:21)
      at Object.complete (file:///Applications/quarto/bin/quarto.js:115409:9)
      at eventLoopTick (ext:core/01_core.js:178:7)
      at async Object.onPostProcess (file:///Applications/quarto/bin/quarto.js:123992:28)
      at async renderFileInternal (file:///Applications/quarto/bin/quarto.js:123976:3)
  Saving _problems/test-Generate-49.R
  
  
  processing file: main_template.qmd
  output file: main_template.knit.md
  
  Closing database connection
  pandoc 
    to: html
    output-file: main_template.html
    standalone: true
    self-contained: true
    section-divs: true
    html-math-method: mathjax
    wrap: none
    default-image-extension: png
    toc: true
    toc-depth: 4
    number-sections: true
    variables: {}
    
  metadata
    document-css: false
    link-citations: true
    date-format: long
    lang: en
    title: ASSURE Full Report
    toc-title: Contents
    
  Output created: main_template.html
  
  [ FAIL 2 | WARN 2 | SKIP 2 | PASS 418 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-Helpers.R:89:1'
  • skip prediction report due to odd linux error (1):
    'test-PredictionReport.R:5:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Backwards.R:18:3'): generatePresentationMultiple old works ─────
  Error in `quarto::quarto_render(input = file.path(intermediateDir, "presentation", "assure_presentation.qmd"), execute_params = list(server = server, username = username, password = password, dbms = dbms, resultsSchema = resultsSchema, dbDetails = dbDetails, lead = lead, team = team, trigger = trigger, safetyQuestion = safetyQuestion, objective = objective, topline1 = topline1, topline2 = topline2, topline3 = topline3, date = date, targetId = targetId, outcomeIds = outcomeIds, cohortNames = cohortNames, cohortIds = cohortIds,      covariateIds = covariateIds, details = details, evaluationText = evaluationText, includeCI = includeCI, includeCharacterization = includeCharacterization, includeCM = includeCM, includeSCCS = includeSCCS, includePLP = includePLP, pathToDriver = pathToDriver))`: ! Error running quarto CLI from R.
  Caused by error in `quarto::quarto_render()`:
  ✖ Error returned by quarto CLI.
    -----------------------------
    
    
    processing file: assure_presentation.qmd
    output file: assure_presentation.knit.md
    
    Closing database connection
    pandoc
    to: revealjs
    output-file: assure_presentation.html
    standalone: true
    self-contained: true
    wrap: none
    default-image-extension: png
    html-math-method:
    method: mathjax
    url: >-
    https://cdn.jsdelivr.net/npm/mathjax@2.7.9/MathJax.js?config=TeX-AMS_HTML-full
    slide-level: 2
    variables:
    
    metadata
    link-citations: true
    width: 1050
    height: 700
    margin: 0.1
    center: false
    navigationMode: linear
    controlsLayout: edges
    controlsTutorial: false
    hash: true
    history: true
    hashOneBasedIndex: false
    fragmentInURL: false
    transition: none
    backgroundTransition: none
    pdfSeparateFragments: false
    lang: en
    auto-stretch: true
    title: ASSURE Analysis
    scrollable: true
    theme:
    - default
    - presentation_style.scss
    logo: img/logo.png
    title-slide-attributes:
    data-background-color: '#EB1700'
    footer: ASSURE Analysis
    slideNumber: true
    showSlideNumber: all
    menu:
    side: left
    numbers: true
    
    [WARNING] Could not fetch resource img/logo.png
    ERROR: Refusing to remove directory
    /private/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/RtmpUGvSgG/working_dir/RtmpCTXGIR/presentation/assure_presentation_files
    that isn't a subdirectory of
    /var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/RtmpUGvSgG/working_dir/RtmpCTXGIR/presentation
    
    Stack trace:
    at safeRemoveDirSync (file:///Applications/quarto/bin/quarto.js:2540:11)
    at file:///Applications/quarto/bin/quarto.js:114469:9
    at Array.forEach (<anonymous>)
    at renderCleanup (file:///Applications/quarto/bin/quarto.js:114467:23)
    at file:///Applications/quarto/bin/quarto.js:115409:44
    at withTiming (file:///Applications/quarto/bin/quarto.js:18977:21)
    at Object.complete (file:///Applications/quarto/bin/quarto.js:115409:9)
    at eventLoopTick (ext:core/01_core.js:178:7)
    at async Object.onPostProcess
    (file:///Applications/quarto/bin/quarto.js:123992:28)
    at async renderFileInternal
    (file:///Applications/quarto/bin/quarto.js:123976:3)
    
  Caused by error:
  ! System command 'quarto' failed
  ── Error ('test-Generate.R:16:3'): generatePresentation ────────────────────────
  Error in `quarto::quarto_render(input = file.path(intermediateDir, "presentation", "assure_presentation.qmd"), execute_params = list(server = server, username = username, password = password, dbms = dbms, resultsSchema = resultsSchema, dbDetails = dbDetails, lead = lead, team = team, trigger = trigger, safetyQuestion = safetyQuestion, objective = objective, topline1 = topline1, topline2 = topline2, topline3 = topline3, date = date, targetId = targetId, outcomeIds = outcomeIds, cohortNames = cohortNames, cohortIds = cohortIds,      covariateIds = covariateIds, details = details, evaluationText = evaluationText, includeCI = includeCI, includeCharacterization = includeCharacterization, includeCM = includeCM, includeSCCS = includeSCCS, includePLP = includePLP, pathToDriver = pathToDriver))`: ! Error running quarto CLI from R.
  Caused by error in `quarto::quarto_render()`:
  ✖ Error returned by quarto CLI.
    -----------------------------
    
    
    processing file: assure_presentation.qmd
    output file: assure_presentation.knit.md
    
    Closing database connection
    pandoc
    to: revealjs
    output-file: assure_presentation.html
    standalone: true
    self-contained: true
    wrap: none
    default-image-extension: png
    html-math-method:
    method: mathjax
    url: >-
    https://cdn.jsdelivr.net/npm/mathjax@2.7.9/MathJax.js?config=TeX-AMS_HTML-full
    slide-level: 2
    variables:
    
    metadata
    link-citations: true
    width: 1050
    height: 700
    margin: 0.1
    center: false
    navigationMode: linear
    controlsLayout: edges
    controlsTutorial: false
    hash: true
    history: true
    hashOneBasedIndex: false
    fragmentInURL: false
    transition: none
    backgroundTransition: none
    pdfSeparateFragments: false
    lang: en
    auto-stretch: true
    title: ASSURE Analysis
    scrollable: true
    theme:
    - default
    - presentation_style.scss
    logo: img/logo.png
    title-slide-attributes:
    data-background-color: '#EB1700'
    footer: ASSURE Analysis
    slideNumber: true
    showSlideNumber: all
    menu:
    side: left
    numbers: true
    
    [WARNING] Could not fetch resource img/logo.png
    ERROR: Refusing to remove directory
    /private/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/RtmpUGvSgG/working_dir/RtmpCTXGIR/presentation/assure_presentation_files
    that isn't a subdirectory of
    /var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T/RtmpUGvSgG/working_dir/RtmpCTXGIR/presentation
    
    Stack trace:
    at safeRemoveDirSync (file:///Applications/quarto/bin/quarto.js:2540:11)
    at file:///Applications/quarto/bin/quarto.js:114469:9
    at Array.forEach (<anonymous>)
    at renderCleanup (file:///Applications/quarto/bin/quarto.js:114467:23)
    at file:///Applications/quarto/bin/quarto.js:115409:44
    at withTiming (file:///Applications/quarto/bin/quarto.js:18977:21)
    at Object.complete (file:///Applications/quarto/bin/quarto.js:115409:9)
    at eventLoopTick (ext:core/01_core.js:178:7)
    at async Object.onPostProcess
    (file:///Applications/quarto/bin/quarto.js:123992:28)
    at async renderFileInternal
    (file:///Applications/quarto/bin/quarto.js:123976:3)
    
  Caused by error:
  ! System command 'quarto' failed
  
  [ FAIL 2 | WARN 2 | SKIP 2 | PASS 418 ]
  Error:
  ! Test failures.
  Execution halted
  Closing database connection
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [8s/10s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/OhdsiReportGenerator.Rcheck/00check.log’
for details.

      125.26 real        79.54 user        14.88 sys